cff-version: 1.2.0 abstract: "

General information

This simulation data belongs to the article:

Precision in iterative modulation enhanced single-molecule localization microscopy

DOI: https://doi.org/10.1016/j.bpj.2022.05.027

This information is also available in README.txt, included in this repository.

Data availability

The simulation code underlying the article can be found at:

https://github.com/qnano/iterative-localization

Data description

The simulation data in this repository, consisting of .npy files, is contained in several .zip files. The title of the .zip files describes which quantity is contained in it. 

Specifically:

If you want to access all the data, including (raw) quantities that are not directly used to compute the results shown in the article, download SimData.zip. SimData.zip contains all data from individual .zip-files, combined for your convenience. Alternatively, you can download all individual .zip-files.

Within the .zip folders, the title of the data contains the simulation parameters it was obtained from. The data titles follow the following format (where the brackets [...] indicate variables):

[prefix]-iter-[parameter itermax]-thetaI-[parameter theta_I]-m-[parameter 100*m]-alpha-[parameter 100*alpha]-thetab-[parameter theta_b].npy

The variables are defined as follows:

For example, the file VTIx-iter-3-thetaI-2000-m-95-alpha-300-thetab-8.npy contains the simulated VTI values of an imeSMLM experiment in the fixed photon budget scenario with 3 iterations, an expected photon budget of 2000 photons, a modulation contrast of 0.95, an aggressiveness parameter of 3 and an expected background of 8 photons/pixel.

The reference table Datasets.xlsx describes which simulation parameters are used in each simulation. It also contains an overview of which datasets are used in each of the figures in the article.

Using existing data

This section describes how to use the simulation data in this repository to reproduce results.

1. Download Datasets.xlsx and place it in the directory "/iterative_localization/". This file describes which simulation parameters are used in each simulation. It also contains an overview of which datasets are used in each of the figures in the article.

2. Download the appropriate (raw and processed) simulation data. Specifically:

  1. CRLBxI.zip
  2. CRLBxM.zip
  3. FT-J.zip
  4. FT-mod.zip
  5. FT-modT.zip
  6. FT-smp.zip
  7. FT-theta.zip
  8. FT-thetaMAP.zip
  9. FT-VTIx.zip
  10. FT-VTIxT.zip
  11. J.zip
  12. smp.zip
  13. theta.zip
  14. thetaMAP.zip
  15. VTIx.zip
  16. VTIxT.zip
" authors: - family-names: Kalisvaart given-names: Dylan orcid: "https://orcid.org/0000-0001-7041-7870" - family-names: Cnossen given-names: Jelmer - family-names: Hung given-names: Shih-Te - family-names: Stallinga given-names: S. (Sjoerd) orcid: "https://orcid.org/0000-0003-4978-3272" - family-names: Verhaegen given-names: Michel - family-names: Smith given-names: Carlas orcid: "https://orcid.org/0000-0003-0591-5093" title: "Data underlying the publication: Precision in iterative modulation enhanced single-molecule localization microscopy" keywords: version: 1 identifiers: - type: doi value: 10.4121/19786735.v1 license: CC BY 4.0 date-released: 2022-06-16